Is this a migrated cluster or a brand new one? I'm guessing you're using
the new AMI?
The migration process supposed to have updated those env.sh paths.

More to the point, is your tophat job failing due to bowtie not being
found? Try adding the path to bowtie executables to tophat's env.sh file as
well and see if that fixes the issue.
On Fri, Jul 12, 2013 at 5:26 PM, Ravpreet Setia
<ravpreet.se...@oicr.on.ca>wrote:
> This may be a problem with the latest Galaxy Cloudman AMI.
>
> Some tools (tophat is one) are failing to run because they cannot be
> found. I have noticed that after launching a new instance with the latest
> AMI, the "<package>/<version>/default" sym-links under /mnt/galaxy/tools
> point to a directory in /mnt/galaxyTools, which does not exist since this
> new AMI merged galaxyTools and galaxyData.
>
> Additionally, even after manually fixing the symlink and the path in the
> env.sh file (it also references galaxyTools), running tophat would fail,
> although now, at least, it can find the program. This may be an issue with
> tophat's XML or python script though, since I fixed Velvet's symlink and
> env.sh and it worked perfectly.
>
> This document explains how the default symlink and env.sh are used by
> Galaxy:
> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
>
> Thanks for any suggestions.
>
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